Cosmopolites sordidus genome assemblies

PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference-based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed Bacterial contamination within intragenic regions of Arthropoda-binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this paper, we demonstrate that in this case, the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of...

本研究采用PacBio HiFi测序（PacBio HiFi sequencing）结合宏基因组分箱（metagenomic binning）技术，构建了蛀茎象甲（Cosmopolites sordidus）的高质量参考基因组。本研究对比了基于k-mer与比对参考序列的分箱前、分箱后两种污染去除方案以清除样本污染。同时，本研究旨在探究分箱后方案是否会在节肢动物分箱重叠群（contigs）的基因内区域中出现弥散分布的细菌污染。经分析，共鉴定出3433个基因，其对应的测序reads被判定为疑似细菌来源。分箱前方案获得的蛀茎象甲（C. sordidus）基因组大小为1.07Gb，包含3089个重叠群，其基因组与蛋白BUSCO（Benchmarking Universal Single-Copy Orthologs）完整单拷贝评分分别为98.6%与97.1%。本研究证实，在此案例中，分箱前方案无需为实施更严格的宏基因组过滤而牺牲组装质量。同时发现，分箱后方案会导致基因内污染程度随测序覆盖度提升而加重，但该污染的发生频率……